Question: differences between Illumina Platinum Variant Calls and NIST variant calls
gravatar for kspata
12 months ago by
kspata70 wrote:

Hi All,

I am validating a bioinformatics pipeline for SNP and INDEL calling. For this purpose I mapped the reads from Illumina Platinum Genome ( to hg38 assembly ( and called variants on a smaller subset region chr19:29,207,790-29,217,448. To verify the detection of these variants I used two data sets

  1. From Illumina Platinum Genome (
  2. From NIST (

There is one variant at location chr19 :29215367 which is detected by variant calling pipeline at frequency > 50%. This variant is present in NIST variant dataset but not in illumina platinum genome.

This variant is also present in the CRAM ( file downloaded from Illumina PG site at frequency 54% as visualized by IGV. variant-in-igv

Should I use NIST variants instead of Illumina PG, as this variant will be shown as False Positive.

Can I merge both these dataets to get more comprehensive variant call. Will it be advisable to merge the two datasets?

I will appreciate an insight into this.

snp vcf • 310 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by kspata70
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